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lh3 / minimap

This repo is DEPRECATED. Please use minimap2, the successor of minimap.
https://github.com/lh3/minimap2
MIT License
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paf to las? #12

Closed ilanshom closed 7 years ago

ilanshom commented 7 years ago

Hi, I am one of the developers of HINGE and we would like to integrate minimap into our pipeline. But we currently work with .las files for the alignments. We noticed that a da2paf converter was discussed here. So we were wondering if any .paf to .las converter has been written. Thanks!

lh3 commented 7 years ago

.las is a binary format without a spec. It seems not a standalone format as it depends on the read database. Generating .las will be a lot harder than the reverse.

govinda-kamath commented 7 years ago

Do you have any script to convert paf to sam? You do seem to have a script to to do the reverse here

lh3 commented 7 years ago

It is not possible to convert minimap PAF to SAM because minimap PAF doesn't compute CIGAR. It is possible to convert minimap2 PAF to SAM if the PAF is generated with CIGAR. However, for read overlapping, minimap2 does not recommend to compute CIGAR for the performance purpose.

ilanshom commented 7 years ago

Thank you for your responses.